You dont need the screen width and height more accurate than a few mm. It sounds like your trying to use that to do something other than what its for. You generally size icons using the sizing screen F8. It has markers to set the size of the icon on a background grid. If your having trouble controlling the rate at which it scales using the arrow keys then press ctrl, and also ctrl and shift at the same time when using arrow keys. If the icon is a specific size you know then under F2 icons and images menu is a set size for icon button where you can enter it numerically. Adjusting the screen dimensions is there just to make it about right size on screen at 1:1 scale so that you can project the screen onto a table top and use 1:60 exact scaling for example. Also it gets the aspect ratio right on different - esp widescreen - monitors. Trying to adjust it to an accuracy of 0.01 of a mm and still feeling like you need to take it into Gimp to fix sounds just wrong. Maybe you should take some screen grabs about what your trying to do and post so we can see.

There is no manual layer ordering. The reason is simple - the program is designed to take these branches of maps which themselves have layers to them in the hierarchy and your able to reuse them in many different places. So if you had to manually do it then every time you moved one full set of layers into a group of another then you would have to manually fix up all the layering. Your saying that your keeps tower is appearing over the keep. That sounds like a good thing to me so maybe again you can take a screen grab of what the issue is.

There are some ways to make things change layer. If you have a tiled array of small icons like bits of cobble and these are supposed to be on the ground and the big towers are then under your cobble then what you can do is make your cobbled floor out of the bits and then use F2 and use the Create New Icon from Screen Image to make one single new icon which is the image of all the little cobbled tiles together. Then as one image its larger than the towers and will snap under them. The other way is to put lots of clear image around the bit of the image thats relevant so that the icon is actually much bigger than the visible part of it. Scale it so the visible bit is the right size and then the icon is big so will drop below layers of other stuff.

In the help under the "four main dialog menus" look for the "the third way..." and it will take you through some pages about it.